Mark,
You can specify an alternate parameters file to use using a command line
option. Type the Comet binary ("comet.exe" I presume) on the command line
without any input arguments to get the usage statement with the command
line options. The "-P" option is to specify the parameter file e.g.
comet.exe -Palternate.parameters *inputfile*.mzML
After each of your searches, you will have to rename your output files,
e.g. *inputfile*.pep.xml, so that they are not overwritten with the
subsequent search. Is this what you're looking for?
Jimmy
On Thursday, June 25, 2020 at 10:52:41 AM UTC-7, Mark Athanason wrote:
>
> Hello,
>
> This may be a stupid question but I'm not great with windows batch
> processing. I'm trying to use Comet to search my MS files where a host of
> different PTMs will be present; as such, I'll need to specify these PTMs in
> various param files and perform the searches sequentially. Is there a way
> to direct comet to the specific param file I want rather than having
> several copies of comet.exe in the mxXML directory?
>
> All the best,
> Mark
>
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